MolNFT v1 · #157651 · protein
Crystal structure of the ligase domain of fungal tRNA ligase TRL1
6N67: “Crystal structure of the ligase domain of fungal tRNA ligase TRL1”. X-ray diffraction, 3 ligands (APC, CL, SO4), 5 pockets (best druggability 0.61). MolNFT v1 #157651 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6N67
- Type
- protein
- Length
- 388 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA ligase
- EC
- 6.5.1.3
- UniProt
- G0S6G2
- Ligands
- APC, CL, SO4
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA ligase (EC 6.5.1.3) | protein | 388 | 37% helix, 24% strand | G0S6G2 |
Ligands and binding sites
- APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · chains A
- CL · Chloride ion · ion · 3 copies · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 265 | 0.61 | 0.80 | 31 | APC, CL |
| 2 | 240 | 0.55 | 0.78 | 28 | empty |
| 3 | 207 | 0.53 | 0.77 | 22 | empty |
| 4 | 99 | 0.42 | 0.77 | 19 | empty |
| 5 | 54 | 0.35 | 0.79 | 16 | empty |
Modifications
Observed in the structure: 2 modified (engineered).
Compared structures
- 6N67 · Crystal structure of the ligase domain of fungal tRNA ligase Trl1 · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt G0S6G2
- Elsewhere: RCSB PDB 6N67 · PDBe 6N67 · UniProt G0S6G2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.